Coupling sensitive \u3cem\u3ein vitro\u3c/em\u3e and in silico techniques to assess cross-reactive CD4\u3csup\u3e+\u3c/sup\u3e T cells against the swine-origin H1N1 influenza virus

The outbreak of the novel swine-origin H1N1 influenza in the spring of 2009 took epidemiologists, immunologists, and vaccinologists by surprise and galvanized a massive worldwide effort to produce millions of vaccine doses to protect against this single virus strain. Of particular concern was the apparent lack of pre-existing antibody capable of eliciting cross-protective immunity against this novel virus, which fueled fears this strain would trigger a particularly far-reaching and lethal pandemic. Given that disease caused by the swine-origin virus was far less severe than expected, we hypothesized cellular immunity to cross-conserved T cell epitopes might have played a significant role in protecting against the pandemic H1N1 in the absence of cross-reactive humoral immunity. In a published study, we used an immunoinformatics approach to predict a number of CD4+ T cell epitopes are conserved between the 2008–2009 seasonal H1N1 vaccine strain and pandemic H1N1 (A/California/04/2009) hemagglutinin proteins. Here, we provide results from biological studies using PBMCs from human donors not exposed to the pandemic virus to demonstrate that pre-existing CD4+ T cells can elicit cross-reactive effector responses against the pandemic H1N1 virus. As well, we show our computational tools were 80–90% accurate in predicting CD4+ T cell epitopes and their HLA-DRB1-dependent response profiles in donors that were chosen at random for HLA haplotype. Combined, these results confirm the power of coupling immunoinformatics to define broadly reactive CD4+ T cell epitopes with highly sensitive in vitro biological assays to verify these in silico predictions as a means to understand human cellular immunity, including cross-protective responses, and to define CD4+ T cell epitopes for potential vaccination efforts against future influenza viruses and other pathogens

Initiating change locally in bullying and aggression through the school environment (INCLUSIVE) trial: update to cluster randomised controlled trial protocol.

BACKGROUND: Systematic reviews suggest that multi-component interventions are effective in reducing bullying victimisation and perpetration. We are undertaking a phase III randomised trial of the INCLUSIVE multi-component intervention. This trial aims to assess the effectiveness and cost-effectiveness of the INCLUSIVE intervention in reducing aggression and bullying victimisation in English secondary schools. This paper updates the original trial protocol published in 2014 (Trials 15:381, 2014) and presents the changes in the process evaluation protocol and the secondary outcome data collection. METHODS: The methods are summarised as follows. DESIGN: cluster randomised trial. PARTICIPANTS: 40 state secondary schools. Outcomes assessed among the cohort of students at the end of year 7 (n = 6667) at baseline. INTERVENTION: INCLUSIVE is a multi-component school intervention including a social and emotional learning curriculum, changes to school environment (an action group comprising staff and students reviews local data on needs to review rules and policies and determine other local actions) and staff training in restorative practice. The intervention will be delivered by schools supported in the first two years by educational facilitators independent of the research team, with a third intervention year involving no external facilitation but all other elements. Comparator: normal practice. OUTCOMES: Primary: Two primary outcomes at student level assessed at baseline and at 36 months: 1. Aggressive behaviours in school: Edinburgh Study of Youth Transitions and Crime school misbehaviour subscale (ESYTC) 2. Bullying and victimisation: Gatehouse Bullying Scale (GBS) Secondary outcomes assessed at baseline, 24 and 36 months will include measures relating to the economic evaluation, psychosocial outcomes in students and staff and school-level truancy and exclusion rates. SAMPLE SIZE: 20 schools per arm will provide 90% power to identify an effect size of 0.25 SD with a 5% significance level. Randomisation: eligible consenting schools were randomised stratified for single-sex versus mixed-sex schools, school-level deprivation and measures of school attainment. DISCUSSION: The trial involves independent research and intervention teams and is supervised by a Trial Steering Committee and a Data Monitoring Committee. TRIAL REGISTRATION: Current Controlled Trials, ISRCTN10751359 . Registered on 11 March 2014

Examining intervention mechanisms of action using mediation analysis within a randomised trial of a whole-school health intervention.

BACKGROUND: Interventions to modify school environments are effective in promoting young people's health across outcomes, but mechanisms are poorly understood. We assessed mediation in a trial of the Learning Together intervention, building on the recent publication of results of effectiveness for reducing bullying and benefits across secondary outcomes and generally good implementation fidelity. METHODS: Within a cluster-randomised trial involving 40 English schools, we examined student-reported and staff-reported school climate and student-reported involvement with delinquent peers at 24-month and 36-month follow-up, assessing the reliability of measures and whether these mediated health outcomes at a final follow-up. RESULTS: Response rates and reliability were good for student-reported but not staff-reported measures. The intervention increased student-reported but not staff-reported-positive school climate but, like effects on student health outcomes, these manifested only at a final follow-up. The intervention reduced student-reported contact with delinquent peers at an interim follow-up. Student-reported potential mediators measured at the interim follow-up were associated with most health outcomes at the final follow-up. Adjustment for student-reported school climate and contact with delinquent peers at the interim follow-up did not reduce the associations between trial arm and our health outcomes. CONCLUSION: Despite being constrained by imperfect measures and by the late manifestation of impacts on student-reported school climate undermining ability to assess mediation, our study for the first time provides tentative evidence that mediation of intervention effects via improved climate and disengagement from delinquent peers is plausible. Our study provides the first evidence from a trial that whole-school interventions may work by modifying school environments and student relationships. TRIAL REGISTRATION NUMBER: ISRCTN10751359

Effects of school environments on student risk-behaviours: evidence from a longitudinal study of secondary schools in England.

BACKGROUND: The theory of human functioning and school organisation proposes that schools with rigid 'boundaries' (weaker relationships), for example, between staff and students, or learning and broader development, engender weaker student school commitment and sense of belonging, particularly among disadvantaged students, leading to greater involvement in risk-behaviours. Existing studies provide some support but rely on a proxy exposure of 'value-added education' and have not explored effects by disadvantage. METHODS: We used longitudinal data from English secondary schools from the control arm of a trial, assessing school-level measures of rigid boundaries, and student commitment and belonging at age 11/12, and student risk-behaviours at age 14/15. RESULTS: Our direct measures were more strongly associated with risk-behaviours than was value-added education. School-level rigid boundaries were associated with increased alcohol use and bullying. Student belonging was more consistently associated with reduced risk-behaviours than was student commitment. Some school effects were greater for students from disadvantaged subgroups defined in terms of poverty, ethnicity and family structure. CONCLUSION: Our results provide direct support for the theory of human functioning and school organisation and suggest a sense of belonging in school might be particularly protective factor among secondary school students. School effects on risk are generally stronger among disadvantaged students as theorised. TRIAL REGISTRATION NUMBER: ISRCTN10751359

Cohort Profile: The Flu Watch Study

Influenza is a common, highly contagious respiratory virus which infects all age groups, causing a range of outcomes from asymptomatic infection and mild respiratory disease to severe respiratory disease and death.1 If infected, the adaptive immune system produces a humoral (antibody) and cell-mediated (T cell) immune response to fight the infection.2 Influenza viruses continually evolve through antigenic drift, resulting in slightly different ‘seasonal’ influenza strains circulating each year. Population-level antibody immunity to these seasonal viruses builds up over time, so in any given season only a proportion of the population is susceptible to the circulating strains. Occasionally, influenza A viruses evolve rapidly through antigenic shift by swapping genes with influenza viruses usually circulating in animals. This process creates an immunologically distinct virus to which the population may have little to no antibody immunity. The virus can result in a pandemic if a large portion of the population is susceptible and the virus is easily spread

Modifying the secondary school environment to reduce bullying and aggression: the INCLUSIVE cluster RCT

BackgroundBullying, aggression and violence among children and young people are some of the most consequential public mental health problems.ObjectivesThe INCLUSIVE (initiating change locally in bullying and aggression through the school environment) trial evaluated the Learning Together intervention, which involved students in efforts to modify their school environment using restorative approaches and to develop social and emotional skills. We hypothesised that in schools receiving Learning Together there would be lower rates of self-reported bullying and perpetration of aggression and improved student biopsychosocial health at follow-up than in control schools.DesignINCLUSIVE was a cluster randomised trial with integral economic and process evaluations.SettingForty secondary schools in south-east England took part. Schools were randomly assigned to implement the Learning Together intervention over 3 years or to continue standard practice (controls).ParticipantsA total of 6667 (93.6%) students participated at baseline and 5960 (83.3%) students participated at final follow-up. No schools withdrew from the study.InterventionSchools were provided with (1) a social and emotional curriculum, (2) all-staff training in restorative approaches, (3) an external facilitator to help convene an action group to revise rules and policies and to oversee intervention delivery and (4) information on local needs to inform decisions.Main outcome measuresSelf-reported experience of bullying victimisation (Gatehouse Bullying Scale) and perpetration of aggression (Edinburgh Study of Youth Transitions and Crime school misbehaviour subscale) measured at 36 months. Intention-to-treat analysis using longitudinal mixed-effects models.ResultsPrimary outcomes – Gatehouse Bullying Scale scores were significantly lower among intervention schools than among control schools at 36 months (adjusted mean difference –0.03, 95% confidence interval –0.06 to 0.00). There was no evidence of a difference in Edinburgh Study of Youth Transitions and Crime scores. Secondary outcomes – students in intervention schools had higher quality of life (adjusted mean difference 1.44, 95% confidence interval 0.07 to 2.17) and psychological well-being scores (adjusted mean difference 0.33, 95% confidence interval 0.00 to 0.66), lower psychological total difficulties (Strengths and Difficulties Questionnaire) score (adjusted mean difference –0.54, 95% confidence interval –0.83 to –0.25), and lower odds of having smoked (odds ratio 0.58, 95% confidence interval 0.43 to 0.80), drunk alcohol (odds ratio 0.72, 95% confidence interval 0.56 to 0.92), been offered or tried illicit drugs (odds ratio 0.51, 95% confidence interval 0.36 to 0.73) and been in contact with police in the previous 12 months (odds ratio 0.74, 95% confidence interval 0.56 to 0.97). The total numbers of reported serious adverse events were similar in each arm. There were no changes for staff outcomes. Process evaluation – fidelity was variable, with a reduction in year 3. Over half of the staff were aware that the school was taking steps to reduce bullying and aggression. Economic evaluation – mean (standard deviation) total education sector-related costs were £116 (£47) per pupil in the control arm compared with £163 (£69) in the intervention arm over the first two facilitated years, and £63 (£33) and £74 (£37) per pupil, respectively, in the final, unfacilitated, year. Overall, the intervention was associated with higher costs, but the mean gain in students’ health-related quality of life was slightly higher in the intervention arm. The incremental cost per quality-adjusted life year was £13,284 (95% confidence interval –£32,175 to £58,743) and £1875 (95% confidence interval –£12,945 to £16,695) at 2 and 3 years, respectively.LimitationsOur trial was carried out in urban and periurban settings in the counties around London. The large number of secondary outcomes investigated necessitated multiple statistical testing. Fidelity of implementation of Learning Together was variable.ConclusionsLearning Together is effective across a very broad range of key public health targets for adolescents.Future workFurther studies are required to assess refined versions of this intervention in other settings.Trial registrationCurrent Controlled Trials ISRCTN10751359.FundingThis project was funded by the National Institute for Health Research (NIHR) Public Health Research programme and will be published in full inPublic Health Research; Vol. 7, No. 18. See the NIHR Journals Library website for further project information. Additional funding was provided by the Educational Endowment Foundation.</jats:sec

Messages that increase women’s intentions to abstain from alcohol during pregnancy: results from quantitative testing of advertising concepts

Background: Public awareness-raising campaigns targeting alcohol use during pregnancy are an important part of preventing prenatal alcohol exposure and Fetal Alcohol Spectrum Disorder. Despite this, there is little evidence on what specific elements contribute to campaign message effectiveness. This research evaluated three different advertising concepts addressing alcohol and pregnancy: a threat appeal, a positive appeal promoting a self-efficacy message, and a concept that combined the two appeals. The primary aim was to determine the effectiveness of these concepts in increasing women’s intentions to abstain from alcohol during pregnancy.Methods: Women of childbearing age and pregnant women residing in Perth, Western Australia participated in a computer-based questionnaire where they viewed either a control or one of the three experimental concepts. Following exposure, participants’ intentions to abstain from and reduce alcohol intake during pregnancy were measured. Other measures assessed included perceived main message, message diagnostics, and potential to promote defensive responses or unintended consequences.Results: The concepts containing a threat appeal were significantly more effective at increasing women’s intentions to abstain from alcohol during pregnancy than the self-efficacy message and the control. The concept that combined threat and self-efficacy is recommended for development as part of a mass-media campaign as it has good persuasive potential, provides a balance of positive and negative emotional responses, and is unlikely to result in defensive or unintended consequences.Conclusions: This study provides important insights into the components that enhance the persuasiveness and effectiveness of messages aimed at preventing prenatal alcohol exposure. The recommended concept has good potential for use in a future campaign aimed at promoting women’s intentions to abstain from alcohol during pregnanc

Integration of copy number and transcriptomics provides risk stratification in prostate cancer : a discovery and validation cohort study

Study data are deposited in NCBI GEO (unique identifier number GSE70770).Background : Understanding the heterogeneous genotypes and phenotypes of prostate cancer is fundamental to improving the way we treat this disease. As yet, there are no validated descriptions of prostate cancer subgroups derived from integrated genomics linked with clinical outcome. Methods : In a study of 482 tumour, benign and germline samples from 259 men with primary prostate cancer, we used integrative analysis of copy number alterations (CNA) and array transcriptomics to identify genomic loci that affect expression levels of mRNA in an expression quantitative trait loci (eQTL) approach, to stratify patients into subgroups that we then associated with future clinical behaviour, and compared with either CNA or transcriptomics alone. Findings : We identified five separate patient subgroups with distinct genomic alterations and expression profiles based on 100 discriminating genes in our separate discovery and validation sets of 125 and 103 men. These subgroups were able to consistently predict biochemical relapse (p = 0.0017 and p = 0.016 respectively) and were further validated in a third cohort with long-term follow-up (p = 0.027). We show the relative contributions of gene expression and copy number data on phenotype, and demonstrate the improved power gained from integrative analyses. We confirm alterations in six genes previously associated with prostate cancer ( MAP3K7, MELK, RCBTB2, ELAC2, TPD52, ZBTB4), and also identify 94 genes not previously linked to prostate cancer progression that would not have been detected using either transcript or copy number data alone. We confirm a number of previously published molecular changes associated with high risk disease, including MYC amplification, and NKX3-1, RB1 and PTEN deletions, as well as over-expression of PCA3 and AMACR, and loss of MSMB in tumour tissue. A subset of the 100 genes outperforms established clinical predictors of poor prognosis (PSA, Gleason score), as well as previously published gene signatures (p = 0.0001). We further show how our molecular profiles can be used for the early detection of aggressive cases in a clinical setting, and inform treatment decisions. Interpretation : For the first time in prostate cancer this study demonstrates the importance of integrated genomic analyses incorporating both benign and tumour tissue data in identifying molecular alterations leading to the generation of robust gene sets that are predictive of clinical outcome in independent patient cohorts.Publisher PDFPeer reviewe

Integration of copy number and transcriptomics provides risk stratification in prostate cancer: A discovery and validation cohort study.

BACKGROUND: Understanding the heterogeneous genotypes and phenotypes of prostate cancer is fundamental to improving the way we treat this disease. As yet, there are no validated descriptions of prostate cancer subgroups derived from integrated genomics linked with clinical outcome. METHODS: In a study of 482 tumour, benign and germline samples from 259 men with primary prostate cancer, we used integrative analysis of copy number alterations (CNA) and array transcriptomics to identify genomic loci that affect expression levels of mRNA in an expression quantitative trait loci (eQTL) approach, to stratify patients into subgroups that we then associated with future clinical behaviour, and compared with either CNA or transcriptomics alone. FINDINGS: We identified five separate patient subgroups with distinct genomic alterations and expression profiles based on 100 discriminating genes in our separate discovery and validation sets of 125 and 103 men. These subgroups were able to consistently predict biochemical relapse (p = 0.0017 and p = 0.016 respectively) and were further validated in a third cohort with long-term follow-up (p = 0.027). We show the relative contributions of gene expression and copy number data on phenotype, and demonstrate the improved power gained from integrative analyses. We confirm alterations in six genes previously associated with prostate cancer (MAP3K7, MELK, RCBTB2, ELAC2, TPD52, ZBTB4), and also identify 94 genes not previously linked to prostate cancer progression that would not have been detected using either transcript or copy number data alone. We confirm a number of previously published molecular changes associated with high risk disease, including MYC amplification, and NKX3-1, RB1 and PTEN deletions, as well as over-expression of PCA3 and AMACR, and loss of MSMB in tumour tissue. A subset of the 100 genes outperforms established clinical predictors of poor prognosis (PSA, Gleason score), as well as previously published gene signatures (p = 0.0001). We further show how our molecular profiles can be used for the early detection of aggressive cases in a clinical setting, and inform treatment decisions. INTERPRETATION: For the first time in prostate cancer this study demonstrates the importance of integrated genomic analyses incorporating both benign and tumour tissue data in identifying molecular alterations leading to the generation of robust gene sets that are predictive of clinical outcome in independent patient cohorts.Cambridge work was funded by a CRUK programme grant awarded to DEN; Swedish work and tissue collections were funded by grants from the Linne Centre for Breast and Prostate Cancer (CRISP, grant 70867901), Karolinska Institutet, the Swedish Research Council (K2010-70X-20430-04-3), and the Swedish Cancer Society (11-0287).This is the final version of the article. It first appeared from Elsevier via http://dx.doi.org/10.1016/j.ebiom.2015.07.01